1
|
Quehenberger J, Shen L, Albers SV, Siebers B, Spadiut O. Sulfolobus - A Potential Key Organism in Future Biotechnology. Front Microbiol 2017; 8:2474. [PMID: 29312184 PMCID: PMC5733018 DOI: 10.3389/fmicb.2017.02474] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/28/2017] [Indexed: 11/13/2022] Open
Abstract
Extremophilic organisms represent a potentially valuable resource for the development of novel bioprocesses. They can act as a source for stable enzymes and unique biomaterials. Extremophiles are capable of carrying out microbial processes and biotransformations under extremely hostile conditions. Extreme thermoacidophilic members of the well-characterized genus Sulfolobus are outstanding in their ability to thrive at both high temperatures and low pH. This review gives an overview of the biological system Sulfolobus including its central carbon metabolism and the development of tools for its genetic manipulation. We highlight findings of commercial relevance and focus on potential industrial applications. Finally, the current state of bioreactor cultivations is summarized and we discuss the use of Sulfolobus species in biorefinery applications.
Collapse
Affiliation(s)
- Julian Quehenberger
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Faculty of Chemistry – Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Faculty of Technical Chemistry, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
| |
Collapse
|
2
|
Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China. Sci Rep 2014; 4:7479. [PMID: 25524763 PMCID: PMC5378992 DOI: 10.1038/srep07479] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 11/25/2014] [Indexed: 01/01/2023] Open
Abstract
Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts.
Collapse
|
3
|
Deive FJ, López E, Rodríguez A, Longo MA, Sanromán MÁ. Targeting the Production of Biomolecules by Extremophiles at Bioreactor Scale. Chem Eng Technol 2012. [DOI: 10.1002/ceat.201100528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
4
|
Purification and characterization of glycerate kinase from the thermoacidophilic archaeonThermoplasma acidophilum: An enzyme belonging to the second glycerate kinase family. BIOTECHNOL BIOPROC E 2006. [DOI: 10.1007/bf03026251] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
5
|
Kim S, Lee SB. Rare codon clusters at 5'-end influence heterologous expression of archaeal gene in Escherichia coli. Protein Expr Purif 2006; 50:49-57. [PMID: 16962338 DOI: 10.1016/j.pep.2006.07.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 07/18/2006] [Accepted: 07/24/2006] [Indexed: 11/28/2022]
Abstract
Proteins from hyperthermophilic microorganisms are attractive candidates for novel biocatalysts because of their high resistance to temperature extremes. However, archaeal genes are usually poorly expressed in Escherichia coli because of differences in codon usage. Genes from the thermoacidophilic archaea Sulfolobus solfataricus and Thermoplasma acidophilum contain high proportions of rare codons for arginine, isoleucine, and leucine, which are recognized by the tRNAs encoded by the argU, ileY, and leuW genes, respectively, and which are rarely used in E. coli. To examine the effects of these rare codons on heterologous expression, we expressed the Sso_gnaD and Tac_gnaD genes from S. solfataricus and T. acidophilum, respectively, in E. coli. The Sso_gnaD product was expressed at very low levels when the open reading frame (ORF) was cloned in pRSET and expressed in E. coli BL21(DE3), and was expressed at much higher levels in the E. coli BL21(DE3)-CodonPlus RIL strain, which contains extra copies of the argU, ileY, and leuW tRNA genes. In contrast, Tac_gnaD was expressed at similar levels in both E. coli strains. Comparison of the Sso_gnaD and Tac_gnaD gene sequences revealed that the 5'-end of the Sso_gnaD sequence was rich in AGA(arg) and ATA(Ile) codons. These codons were replaced with the codons commonly used in E. coli by polymerase chain reaction-mediated site-directed mutagenesis. The results of expression studies showed that a non-tandem repeat of rare codons is critical in the observed interference in heterologous expression of this gene. We concluded that the level of heterologous expression of Sso_gnaD in E. coli was limited by the clustering of the rare codons in the ORF, rather than on the rare codon frequency.
Collapse
Affiliation(s)
- Seonghun Kim
- School of Environmental Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, Republic of Korea
| | | |
Collapse
|
6
|
Salo-Zieman VLA, Sivonen T, Plumb JJ, Haddad CM, Laukkanen K, Kinnunen PHM, Kaksonen AH, Franzmann PD, Puhakka JA. Characterization of a thermophilic sulfur oxidizing enrichment culture dominated by a Sulfolobus sp. obtained from an underground hot spring for use in extreme bioleaching conditions. J Ind Microbiol Biotechnol 2006; 33:984-94. [PMID: 16767461 DOI: 10.1007/s10295-006-0144-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 05/09/2006] [Indexed: 11/28/2022]
Abstract
A thermoacidophilic elemental sulfur and chalcopyrite oxidizing enrichment culture VS2 was obtained from hot spring run-off sediments of an underground mine. It contained only archaeal species, namely a Sulfolobus metallicus-related organism (96% similarity in partial 16S rRNA gene) and Thermoplasma acidophilum (98% similarity in partial 16S rRNA gene). The VS2 culture grew in a temperature range of 35-76 degrees C. Sulfur oxidation by VS2 was optimal at 70 degrees C, with the highest oxidation rate being 99 mg S(0 )l(-1 )day(-1). At 50 degrees C, the highest sulfur oxidation rate was 89 mg l(-1 )day(-1 )(in the presence of 5 g Cl(-) l(-1)). Sulfur oxidation was not significantly affected by 0.02-0.1 g l(-1) yeast extract or saline water (total salinity of 0.6 M) that simulated mine water at field application sites with availability of only saline water. Chloride ions at a concentration above 10 g l(-1) inhibited sulfur oxidation. Both granular and powdered forms of sulfur were bioavailable, but the oxidation rate of granular sulfur was less than 50% of the powdered form. Chalcopyrite concentrate oxidation (1% w/v) by the VS2 resulted in a 90% Cu yield in 30 days.
Collapse
Affiliation(s)
- Virpi L A Salo-Zieman
- Institute of Environmental Engineering and Biotechnology, Tampere University of Technology, 33101 Tampere, Finland.
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Wiedenheft B, Mosolf J, Willits D, Yeager M, Dryden KA, Young M, Douglas T. An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus. Proc Natl Acad Sci U S A 2005; 102:10551-6. [PMID: 16024730 PMCID: PMC1175829 DOI: 10.1073/pnas.0501497102] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Evolution of an oxygenic atmosphere required primordial life to accommodate the toxicity associated with reactive oxygen species. We have characterized an archaeal antioxidant from the hyperthermophilic acidophile Sulfolobus solfataricus. The amino acid sequence of this approximately 22-kDa protein shares little sequence similarity with proteins with known function. However, the protein shares high sequence similarity with hypothetical proteins in other archaeal and bacterial genomes. Nine of these hypothetical proteins form a monophyletic cluster within the broad superfamily of ferritin-like diiron-carboxylate proteins. Higher order structural predictions and image reconstructions indicate that the S. solfataricus protein is structurally related to a class of DNA-binding protein from starved cells (Dps). The recombinant protein self assembles into a hollow dodecameric protein cage having tetrahedral symmetry (SsDps). The outer shell diameter is approximately 10 nm, and the interior diameter is approximately 5 nm. Dps proteins have been shown to protect nucleic acids by physically shielding DNA against oxidative damage and by consuming constituents involved in Fenton chemistry. In vitro, the assembled archaeal protein efficiently uses H2O2 to oxidize Fe(II) to Fe(III) and stores the oxide as a mineral core on the interior surface of the protein cage. The ssdps gene is up-regulated in S. solfataricus cultures grown in iron-depleted media and upon H2O2 stress, but is not induced by other stresses. SsDps-mediated reduction of hydrogen peroxide and possible DNA-binding capabilities of this archaeal Dps protein are mechanisms by which S. solfataricus mitigates oxidative damage.
Collapse
Affiliation(s)
- Blake Wiedenheft
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | | | | | | | | | | | | |
Collapse
|
8
|
Kim S, Lee S. Identification and characterization of Sulfolobus solfataricus D-gluconate dehydratase: a key enzyme in the non-phosphorylated Entner-Doudoroff pathway. Biochem J 2005; 387:271-80. [PMID: 15509194 PMCID: PMC1134955 DOI: 10.1042/bj20041053] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The extremely thermoacidophilic archaeon Sulfolobus solfataricus utilizes D-glucose as a sole carbon and energy source through the non-phosphorylated Entner-Doudoroff pathway. It has been suggested that this micro-organism metabolizes D-gluconate, the oxidized form of D-glucose, to pyruvate and D-glyceraldehyde by using two unique enzymes, D-gluconate dehydratase and 2-keto-3-deoxy-D-gluconate aldolase. In the present study, we report the purification and characterization of D-gluconate dehydratase from S. solfataricus, which catalyses the conversion of D-gluconate into 2-keto-3-deoxy-D-gluconate. D-Gluconate dehydratase was purified 400-fold from extracts of S. solfataricus by ammonium sulphate fractionation and chromatography on DEAE-Sepharose, Q-Sepharose, phenyl-Sepharose and Mono Q. The native protein showed a molecular mass of 350 kDa by gel filtration, whereas SDS/PAGE analysis provided a molecular mass of 44 kDa, indicating that D-gluconate dehydratase is an octameric protein. The enzyme showed maximal activity at temperatures between 80 and 90 degrees C and pH values between 6.5 and 7.5, and a half-life of 40 min at 100 degrees C. Bivalent metal ions such as Co2+, Mg2+, Mn2+ and Ni2+ activated, whereas EDTA inhibited the enzyme. A metal analysis of the purified protein revealed the presence of one Co2+ ion per enzyme monomer. Of the 22 aldonic acids tested, only D-gluconate served as a substrate, with K(m)=0.45 mM and V(max)=0.15 unit/mg of enzyme. From N-terminal sequences of the purified enzyme, it was found that the gene product of SSO3198 in the S. solfataricus genome database corresponded to D-gluconate dehydratase (gnaD). We also found that the D-gluconate dehydratase of S. solfataricus is a phosphoprotein and that its catalytic activity is regulated by a phosphorylation-dephosphorylation mechanism. This is the first report on biochemical and genetic characterization of D-gluconate dehydratase involved in the non-phosphorylated Entner-Doudoroff pathway.
Collapse
Affiliation(s)
- Seonghun Kim
- *School of Environmental Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea
- †Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea
| | - Sun Bok Lee
- *School of Environmental Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea
- †Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea
- ‡Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea
- To whom correspondence should be addressed (email )
| |
Collapse
|
9
|
Kim KW, Lee SB. Inhibitory effect of Maillard reaction products on growth of the aerobic marine hyperthermophilic archaeon Aeropyrum pernix. Appl Environ Microbiol 2003; 69:4325-8. [PMID: 12839824 PMCID: PMC165203 DOI: 10.1128/aem.69.7.4325-4328.2003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It was found that the growth of Aeropyrum pernix was severely inhibited in a medium containing reducing sugars and tryptone due to the formation of Maillard reaction products. The rate of the Maillard browning reaction was markedly enhanced under aerobic conditions, and the addition of Maillard reaction products to the culture medium caused fatal growth inhibition.
Collapse
Affiliation(s)
- Kee Woung Kim
- Department of Chemical Engineering. Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Korea
| | | |
Collapse
|
10
|
Park CB, Ryu DDY, Lee SB. Inhibitory effect of L-pyroglutamate on extremophiles: correlation with growth temperature and pH. FEMS Microbiol Lett 2003; 221:187-90. [PMID: 12725925 DOI: 10.1016/s0378-1097(03)00213-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
L-Pyroglutamate (PGA) is naturally occurring from L-glutamate solution with accelerated formation rate under high temperature and low pH. Even though PGA has been identified as a neurotoxic agent on brain cells, the effect of PGA on the growth of microorganisms is rarely known. Here various kinds of microorganisms differing in their optimal growth temperature, pH, phylogeny, and isolated biotope were investigated for the effect of PGA. We found that growth of thermoacidophiles, including both archaea and bacteria, was seriously inhibited by the presence of PGA, and the extent of the inhibitory effect was closely related with growth temperature and pH. Interestingly, only microbes that grow at high temperature and low pH are inhibited by PGA, while this compound may stimulate growth rates of organisms that live at neutral pH and low temperature.
Collapse
Affiliation(s)
- Chan Beum Park
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang, South Korea
| | | | | |
Collapse
|
11
|
Woung Kim K, Bok Lee S. Growth of the hyperthermophilic marine archaeon Aeropyrum pernix in a defined medium. J Biosci Bioeng 2003. [DOI: 10.1016/s1389-1723(03)80172-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
12
|
Abstract
The discovery of life in seemingly prohibitive environments continues to challenge conventional concepts of the growth-limiting conditions of many cellular organisms. The diversity of extremophiles has barely been tapped -estimates generally agreeing that <1% of the microorganisms in the environment have been cultivated in pure cultures to date. The production of extremophilic biomass is very important to provide sufficient material for enzyme and biomolecule isolation and characterization, eventually revealing particular features of industrial interest. Hence, special equipment and custom-tailored processes have been developed and are currently under evaluation for the improvement of fermentation productivity. Despite the remarkable opportunities that these uncommon organisms present for biotechnological applications only few instances can be reported for actual exploitation. This lack of progress from the research findings at a laboratory-scale to the actual development of pilot and large-scale production is correlated with the difficulties encountered in extremophile cultivations. Here, we report recent achievements in the production of biomass and related enzymes and biomolecules from extremophile sources, especially focusing on the application of novel fermentation strategies.
Collapse
Affiliation(s)
- Chiara Schiraldi
- Biotechnology and Molecular Biology Unit, Dept of Experimental Medicine, Faculty of Medicine, Second University of Naples, Italy
| | | |
Collapse
|
13
|
Park CB, Lee SB, Ryu DD. L-pyroglutamate spontaneously formed from L-glutamate inhibits growth of the hyperthermophilic archaeon Sulfolobus solfataricus. Appl Environ Microbiol 2001; 67:3650-4. [PMID: 11472943 PMCID: PMC93067 DOI: 10.1128/aem.67.8.3650-3654.2001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identification of physiological and environmental factors that limit efficient growth of hyperthermophiles is important for practical application of these organisms to the production of useful enzymes or metabolites. During fed-batch cultivation of Sulfolobus solfataricus in medium containing L-glutamate, we observed formation of L-pyroglutamic acid (PGA). PGA formed spontaneously from L-glutamate under culture conditions (78 degrees C and pH 3.0), and the PGA formation rate was much higher at an acidic or alkaline pH than at neutral pH. It was also found that PGA is a potent inhibitor of S. solfataricus growth. The cell growth rate was reduced by one-half by the presence of 5.1 mM PGA, and no growth was observed in the presence of 15.5 mM PGA. On the other hand, the inhibitory effect of PGA on cell growth was alleviated by addition of L-glutamate or L-aspartate to the medium. PGA was also produced from the L-glutamate in yeast extract; the PGA content increased to 8.5% (wt/wt) after 80 h of incubation of a yeast extract solution at 78 degrees C and pH 3.0. In medium supplemented with yeast extract, cell growth was optimal in the presence of 3.0 g of yeast extract per liter, and higher yeast extract concentrations resulted in reduced cell yields. The extents of cell growth inhibition at yeast extract concentrations above the optimal concentration were correlated with the PGA concentration in the culture broth. Although other structural analogues of L-glutamate, such as L-methionine sulfoxide, glutaric acid, succinic acid, and L-glutamic acid gamma-methyl ester, also inhibited the growth of S. solfataricus, the greatest cell growth inhibition was observed with PGA. We also observed that unlike other glutamate analogues, N-acetyl-L-glutamate enhanced the growth of S. solfataricus. This compound was stable under cell culture conditions, and replacement of L-glutamate with N-acetyl-L-glutamate in the medium resulted in increased cell density.
Collapse
Affiliation(s)
- C B Park
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Korea
| | | | | |
Collapse
|
14
|
Park CB, Lee SB. Effects of exogenous compatible solutes on growth of the hyperthermophilic archaeon Sulfolobus solfataricus. J Biosci Bioeng 2000; 89:318-22. [PMID: 16232752 DOI: 10.1016/s1389-1723(00)88952-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/1999] [Accepted: 12/24/1999] [Indexed: 11/21/2022]
Abstract
Six known compatible solutes as well as twenty L-amino acids were individually added to a glucose minimal medium and their effects on the growth of Sulfolobus solfataricus (DSM 1617) were examined. Among the compatible solutes tested, putrescine, trehalose, and l-glutamate enhanced the growth of S. solfataricus. On the other hand, glycine betaine, choline, and L-proline showed little or no influence on cell growth. When cells were grown in the glucose medium supplemented with trehalose or L-glutamate, S. solfataricus preferentially utilized the compatible solute over glucose. The growth-enhancement effect of L-glutamate was also observed to be dependent on the glucose concentration in the medium: growth enhancement was higher when the concentration of glucose was low and gradually decreased with increasing glucose concentration. Interestingly, the effects of amino acids on cell growth differed markedly depending on the chemical nature of the amino acid added. While acidic amino acids-L-glutamate and L-aspartate-enhanced the growth rate, almost no growth was observed in the presence of glycine, L-leucine, L-valine, L-phenylalanine, L-threonine, L-methionine, or L-cysteine. Among all the low-molecular-weight solutes tested in this study, the growth-stimulation effect was most profound in the presence of L-glutamate. When S. solfataricus cells were grown in a glucose (1.0 g/l) medium supplemented with 3.0 g/l L-glutamate, the maximal cell density and growth rate were about 3.2- and 2.3-fold higher than those obtained without L-glutamate.
Collapse
Affiliation(s)
- C B Park
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Korea
| | | |
Collapse
|
15
|
Cultivation of the hyperthermophilic archaeonSulfolobus solfataricus in low-salt media. BIOTECHNOL BIOPROC E 1999. [DOI: 10.1007/bf02931908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|